Sweetpotato virus disease (SPVD), a complex of Sweet potato chlorotic stunt virus (SPCSV; Crinivirus) and Sweet potato feathery mottle virus (SPFMV; Potyvirus) causes high yield losses in sub-Saharan Africa (SSA). The development of resistant cultivars to SPVD has been limited by the complex sweetpotato [Ipomoea batatas (L.) Lam. var. batatas] genetics and high levels of mutations in the causal viruses. The objectives of this study were to understand the inheritance of SPVD resistance and identify simple-sequence repeat (SSR) markers associated with its resistance in a biparental sweetpotato mapping population. A total of 287 progeny and parents of the ‘New Kawogo’ × ‘Beaure-gard’ population were genotyped with 250 SSR markers and phenotyped for SPVD resistance at three sites and two seasons in Uganda. The broad-sense heritability for SPVD resistance was 0.51. Two progeny showed positive transgressive segregation for overall genotype mean SPVD severity across sites and seasons. A total of seven SSR markers were significantly associated with SPVD resistance in this population. These markers and other SSRs need to be used to fine map the quantitative trait loci (QTL) of SPVD resistance for future implementation of marker-assisted selection (MAS) for SPVD resistance in sweetpotato.